Share this page!

Enter URL or ID to Unroll

You can paste full URL like: https://x.com/threadreaderapp/status/1644127596119195649
or just the ID like: 1644127596119195649

How to get URL link on X (Twitter) App

  1. On the Twitter thread, click on or icon on the bottom
  2. Click again on or Share Via icon
  3. Click on Copy Link to Tweet
  4. Paste it above and click "Unroll Thread"!
  5. More info at Twitter Help
Caleb Lareau Profile picture
Caleb Lareau
@CalebLareau
Assistant Professor at Memorial Sloan Kettering. Interested in computational and translational immunology. cat dad.
Jun 29, 2023 • 22 tweets • 8 min read
Out today in @NatureGenet, our work utilizing single-cell multi-omics to define specific immune cell subsets that experience purifying selection against pathogenic mitochondrial DNA. Check out a thread about this work below: 1/22nature.com/articles/s4158… I'm so grateful to have worked with a terrific team of co-authors. A special thanks to @LeifLudwig (and his new group!), the @Agarwal_Lab for enabling this work with precious patient samples, and supervision and support from @Satpathology, @bloodgenes, and Aviv Regev 🙏 2/22
Mar 31, 2021 • 25 tweets • 8 min read
I'm genuinely excited to see the extension of methods to discern clonal structure from mtDNA variants-- something that I've thought about over the years. However, I'm going to comment on a couple of points in this pre-print to hopefully show why mtDNA tracing isn't easy 1/n Disclosure: I am the author of mgatk, a method that is compared against in this new approach (Mquad), so I must admit that I was a bit peeved by the statement "there is a lack of effective computational methods to identify informative mtDNA variants" (to qualify this thread) 2/n
Oct 30, 2019 • 31 tweets • 10 min read
A common assumption in #singlecell data is that 1 cell = 1 barcode. You've heard of cell doublets, but what about barcode doublets? In work with the great team of Sai Ma, @fabianamduarte, and @JD_Buenrostro, we quantify this effect: biorxiv.org/content/10.110…. Thread: 1/n In this paper, we coin the term 'barcode multiplets' to describe instances where a barcode was derived from a droplet with more than one high-quality oligonucleotide sequence. We use the term multiplet as we often find instances where there are more than two barcodes! 2/n
Feb 20, 2019 • 20 tweets • 5 min read


Thanks @aayushraman @tangming2005. Here's a few thoughts on how I see the landscape of tools (thread) 1/n In HiChIP data analyses, there are two primary problems that we are trying to solve. A) Which anchors (i.e. genomic loci) should be used as a feature set and B) which loops (i.e. interactions between pairs of loci) are important in the data. 2/n